SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q6P5B0 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MGRSGKLPSGVSAKLKRWKKGHSSDSNPATCRHRQAARSRFFSRPSGKSD    50
  51  LTVDAVKLHNELQSGTLSLGKSQAPETTMDQDPEVAFTEKSSGTFLSGLS   100
 101  DCTNVTFSKVQRFWESNSAAHKEICAVLAAVTEVIRSQGGKETETEYFAA   150
 151  LMTTMEAVESPESLAAVAYLLNLVLKRVPSPVLMKKFSDTSKAFMDIMSA   200
 201  QASSGSTSALRWVLSCLAILLRKQDLEAWGYPITLQVYHGLLSFTVHAKP   250
 251  KIRKAAQHGVCSVLKGSDFMFGEKAPAHHPAAVSTAKFCIQEIEKSGGSK   300
 301  EATTTLHMLTLLKDMLPCFPEGLVKSCSETLLRVMTLNHVLVTACAMQAF   350
 351  HNLFHAKPSPSTLSAELNAQIVTALYDYVPSENDLQPLLAWLKVMEKAHI   400
 401  NLVRLQRDLGLGHLARFFGTAVTCLLSPHSQVAAAATQTLKEILKECVAP   450
 451  HIADIGSVTSSASGPPQYITKMFRAVEEGLTYKFHAAWSSVLQLLGVFFE   500
 501  ACGKQAHPVMKKCLQSLCDLRLSPHFPHTAALDQAVGAAVTSMGPEVVLQ   550
 551  AVPLEIDGSEETLDFPRSWLLPVIRDHVRETRLGFFTTYFLPLATTLKRK   600
 601  AMDLAQAGSTVESKIYDTLQWQIWTLLPGFCTRPTDVAASFKGLARTLGT   650
 651  AINERPDLRVTVCQALRTLITKGCEAEADRAEVSRFAKNFLPILFNLYGQ   700
 701  PVAAGEAAAPRRAVLETIKTYLTITEAQLVNSFLEKATEKVLDPASSDFT   750
 751  RLSVLDLVVALAPYSDEAAISKLYSTIRPYLESKVHGVQKKAYRVLEEVC   800
 801  ASSQGPAARFVQSHLDDLKKTLLDSLRTTSSPAKRPRLKCLIHIVKTLSA   850
 851  EHEEFIAALIPEVILCTKEVSVGARKSAFTLLVEMGHAFLRFGSNQEDAL   900
 901  QRYLVLIYPGLLGAVTTVSCSILALTHLLFEFKGLMGTSTVEQLLENVCL   950
 951  LLASRTRDVVKSALGFIKVAVVVMDVVHLAKHVQLVMEAIGKLSDDMRRH  1000
1001  FRMKLRNLFIKFTRKFGFELVKGLLPAEYHKVLINIRKAETRAKKHRALS  1050
1051  QAAVEEEEEEEEEEEPVQSKGDSIEEILADSEDEDEEEERGRGKEQRKLA  1100
1101  RQRSRAWLKEGGGDEPLNFLDPKVAHRVLATQPGPGRGKKRDHGFKLSAD  1150
1151  GRLIIREEEDGNKVEEEDGTKGEDEDMTDAMEDASVRSKKKLKRQREDEE  1200
1201  DELEIPPRYQAGGSGIHRPVAKKAAPGAEYKAKKAKGDVKKKGRLDPYAY  1250
1251  VPLNRSKLNRRKKVKLQGQFKGLVKATQRGSQAGHKLRRKDRRRP       1295

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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